An interactive web-based Pseudomonas aeruginosa genome database: discovery of new genes, pathways and structures

• Published in: Microbiology (Society for General Microbiology) Vol. 146; no. 10; pp. 2351 - 2364
• Main Authors: Croft, Larry, Beatson, Scott A, Whitchurch, Cynthia B, Huang, Bixing, Blakeley, Robert L, Mattick, John S
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01-10-2000; Society for General Microbiology
• Subjects: Adhesins, Bacterial - genetics; Adhesins, Bacterial - metabolism; Amino Acid Sequence - genetics; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacteriology; Biological and medical sciences; Chemotaxis - genetics; Databases, Factual; Fimbriae, Bacterial - genetics; Fimbriae, Bacterial - metabolism; Fundamental and applied biological sciences. Psychology; Genetics; Genome, Bacterial; Hemagglutinins - genetics; Hemagglutinins - metabolism; Internet; Microbiology; Molecular Sequence Data; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Pseudomonas aeruginosa - metabolism; Pseudomonas aeruginosa - ultrastructure; Pseudomonadales; Gene; Nucleotide sequence; Database; Bacteria; Pseudomonadaceae; Pseudomonas aeruginosa; Functional analysis; Genome; Web site; Aminoacid sequence
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/00221287-146-10-2351

Centre for Functional and Applied Genomics, Institute for Molecular Bioscience 1 and Department of Biochemistry 2 , University of Queensland, Brisbane, QLD 4072, Australia
Author for correspondence: John S. Mattick. Tel: [phone]. Fax: [phone]. e-mail: j.mattick{at}imb.uq.edu.au
Using the complete genome sequence of Pseudomonas aeruginosa PAO1, sequenced by the Pseudomonas Genome Project (ftp://ftp.pseudomonas.com/data/pacontigs.121599), a genome database (http://pseudomonas.bit.uq.edu.au/) has been developed containing information on more than 95% of all ORFs in Pseudomonas aeruginosa . The database is searchable by a variety of means, including gene name, position, keyword, sequence similarity and Pfam domain. Automated and manual annotation, nucleotide and peptide sequences, Pfam and SMART domains (where available), Medline and GenBank links and a scrollable, graphical representation of the surrounding genomic landscape are available for each ORF. Using the database has revealed, among other things, that P. aeruginosa contains four chemotaxis systems, two novel general secretion pathways, at least three loci encoding F17-like thin fimbriae, six novel filamentous haemagglutinin-like genes, a number of unusual composite genetic loci related to vgr / Rhs elements in Escherichia coli , a number of fix -like genes encoding a micro-oxic respiration system, novel biosynthetic pathways and 38 genes containing domains of unknown function (DUF1/DUF2). It is anticipated that this database will be a useful bioinformatic tool for the Pseudomonas community that will continue to evolve.
Keywords: proteome, gene families, regulators, adhesins, type II secretion Abbreviations: FHA, filamentous haemagglutinin; MCP, methyl-accepting chemotaxis protein